Jimmy Shen

Sure Mark. You need a reference image by the way, so you can see what will happen before and after you apply the transformation matrix. Here's the example:

1. Download "avg152T1_RL_nifti.nii" from NIfTI site. I use it as reference image.

2. View how the reference image looks like: nii=load_nii('avg152T1_RL_nifti.nii');
view_nii(nii);

3. Assume that I have a Transformation Matrix, which will let the reference image turn 30 degree counter-clockwise on XY plane, here will be the matrix: T=[cos(pi/6) -sin(pi/6) 0; sin(pi/6) cos(pi/6) 0; 0 0 1];

4. Get old_xyz from reference image: rl=load_untouch_nii('avg152T1_RL_nifti.nii');
old_xyz=[rl.hdr.hist.srow_x(1:3);rl.hdr.hist.srow_y(1:3);rl.hdr.hist.srow_z(1:3)];

5. Apply your transformation matrix, and save new_xyz into a new image: new_xyz=T*old_xyz; rl.hdr.hist.srow_x(1:3)=new_xyz(1,:); rl.hdr.hist.srow_y(1:3)=new_xyz(2,:); rl.hdr.hist.srow_z(1:3)=new_xyz(3,:); save_untouch_nii(rl, 'rl30.nii'); Now you already have the "rl30.nii", which is a transformed NIfTI image can be used anywhere.

6. In order to view this image using my toolbox, you need to reslice it: reslice_nii('rl30.nii', 'rl30b.nii'); Now, you can load and view the rotated image: rl30b=load_nii('rl30b.nii'); view_nii(rl30b);

Hopefully this answers your questions.

My geotiffwrite can only write a rectangular dataset into the file. As long as your sub-region is a rectangular dataset, you should be able to write it into a separate file.

MATLAB finally has its own "geotiffwrite" function. So I suggest you use its geotiffread / geotiffwrite pair to load your Antarctica background, and superimpose your ship track data on top, and then re-write the entire data into GeoTIFF format using Matlab's geotiffwrite function.

I am currently no longer working in GeoScience field, so I am afraid that I cannot provide you with more useful advise.

Sure Mark. You need a reference image by the way, so you can see what will happen before and after you apply the transformation matrix. Here's the example:

1. Download "avg152T1_RL_nifti.nii" from NIfTI site. I use it as reference image.

2. View how the reference image looks like: nii=load_nii('avg152T1_RL_nifti.nii');
view_nii(nii);

3. Assume that I have a Transformation Matrix, which will let the reference image turn 30 degree counter-clockwise on XY plane, here will be the matrix: T=[cos(pi/6) -sin(pi/6) 0; sin(pi/6) cos(pi/6) 0; 0 0 1];

4. Get old_xyz from reference image: rl=load_untouch_nii('avg152T1_RL_nifti.nii');
old_xyz=[rl.hdr.hist.srow_x(1:3);rl.hdr.hist.srow_y(1:3);rl.hdr.hist.srow_z(1:3)];

5. Apply your transformation matrix, and save new_xyz into a new image: new_xyz=T*old_xyz; rl.hdr.hist.srow_x(1:3)=new_xyz(1,:); rl.hdr.hist.srow_y(1:3)=new_xyz(2,:); rl.hdr.hist.srow_z(1:3)=new_xyz(3,:); save_untouch_nii(rl, 'rl30.nii'); Now you already have the "rl30.nii", which is a transformed NIfTI image can be used anywhere.

6. In order to view this image using my toolbox, you need to reslice it: reslice_nii('rl30.nii', 'rl30b.nii'); Now, you can load and view the rotated image: rl30b=load_nii('rl30b.nii'); view_nii(rl30b);

Hopefully this answers your questions.

thank you very much Jimmy